Re: [AMBER] periodic box drifted during NVE run

From: David A Case <>
Date: Wed, 2 Jul 2014 07:40:16 -0400

On Tue, Jul 01, 2014, Quynh Vo wrote:

> Thank you so much for your suggestion Dr. Case. The center command works
> well. Now my concern is if the center command affects the diffusion
> coefficient value of the system. Now I got a value that is 10 times
> smaller than the expected value. Is it more due to the force field? I
> used GAFF. Is there anyway to improve the self diffusion coefficient?

It's not clear what kind of fluid you have, or how you know what the "expected
value" is. I'd suggest doing a simulation water, where there is a large
literature on the self-diffusion coefficients for various force-field models.
Make sure you can reproduce those.

It's actually unusual to see significant box drift: are you sure you don't
have the "Flying ice cube" problem?


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Received on Wed Jul 02 2014 - 05:00:03 PDT
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